Genetic study Population changes in northern Italy from the Iron Age to Modern Times

[Pax Augusta]

Anyone want to explain this from the genetic point of view.

There is nothing new with respect to the thesis that northern Italians and modern Tuscans, being further north genetically than the C6 cluster, had a contribution arrived from the north.

 

[Vallicanus]

There is nothing new with respect to the thesis that northern Italians and modern Tuscans, being further north genetically than the C6 cluster, had a contribution arrived from the north.

The Germanic element in Italy is probably closer to 5-10 %, if that.

 

[Stefano]

Why is the Langobard element as high as 20-30 per cent in North Italians and Tuscans?

It is not, as haplogroups clearly shows. It is inflated in the model because it is a simple two way of italian and germanic, lacking the proper iron age component which is our ethnic basis(cisalpine celt,etruscan,ligurian,raethian...). 5-10 as you've said is a reasonable amount, in line with ydna.

 

[Pax Augusta]

The Germanic element in Italy is probably closer to 5-10 %, if that.

Yes, of course. We have already said this dozens of times. Germanic uniparental markers in Italy are 5-10% at most. However, there is also to be said that this is not corroborating. One can give dozens and dozens of different examples. Sardinians are 40% I2a, a mesolithic marker but EEF is higher than WHG in Sardinians. And so on. The distribution of current uniparental markers do not exactly correspond to contributions in autosomal DNA.

Going back to the one above, it is only a statistical model. 30-20% is the difference between northern Italians/Tuscans with the C6 cluster using a northern European source. Since there is still a lack of published samples for the Iron Age from 3/4 of Italy it should only be taken as a reference model, not as a definitive answer.

 

[Vallicanus]

It is not, as haplogroups clearly shows. It is inflated in the model because it is a simple two way of italian and germanic, lacking the proper iron age component which is our ethnic basis(cisalpine celt,etruscan,ligurian,raethian...). 5-10 as you've said is a reasonable amount, in line with ydna.

AI Coplot using my G25 coordinates, gives me a predominantly coastal Etruscan ancestry eg samples like VET001 from Vetulonia plus a little Imperial Roman and Cisalpine Celtic but little or no Germanic Langobard.

 

[Jovialis]

library(admixtools)
library(tidyverse)

prefix   <- "C:/Users/jovialis/Documents/Bioinformatics/Jovialis_HO_merge_PLINK/merged_HO"
f2_dir   <- "C:/Users/jovialis/Documents/Bioinformatics/Jovialis_HO_merge_PLINK/f2_blocks"

target   <- "Italian_North.HO"
left     <- c(
    "Italy_North_EarlyMedieval_Langobards_1.AG",
    "C6_Central_Italy_Medieval_Central_Mediterranean"
)

outgroups <- c(
    "Ethiopia_4500BP.AG", "Russia_UstIshim_IUP.DG", "Italy_Epigravettian.AG.BY.AA", "Russia_YuzhniyOleniyOstrov_Mesolithic.AG", "Russia_MA1_UP.SG", "Georgia_Satsurblia_LateUP.SG", "Jordan_PPNB.AG")

mypops <- c(target, left, outgroups)

extract_f2(
    prefix, f2_dir,
    pops      = mypops,
    overwrite = TRUE,
    auto_only = TRUE,
    blgsize   = 0.05
)

f2_blocks <- f2_from_precomp(
    f2_dir,
    pops   = mypops,
    afprod = TRUE
)

qpwave_results <- qpwave(
    f2_blocks,
    left    = left,
    right   = outgroups,
    verbose = TRUE
)
print(qpwave_results$rankdrop)

min_p <- min(qpwave_results$rankdrop$p, na.rm = TRUE)

if (!is.na(min_p) && min_p > 0.05) {
    res_geno <- qpadm(
        prefix,
        left      = left,
        right     = outgroups,
        target    = target,
        allsnps   = TRUE,
        auto_only = TRUE,
        verbose   = TRUE,
        return_f4 = TRUE
    )
    print(res_geno$weights)
    print(res_geno$popdrop)
} else {
    res_geno <- qpadm(
        prefix,
        left      = left,
        right     = outgroups,
        target    = target,
        allsnps   = TRUE,
        auto_only = TRUE,
        verbose   = TRUE,
        return_f4 = TRUE
    )
    res_f2 <- qpadm(
        f2_blocks,
        left      = left,
        right     = outgroups,
        target    = target,
        verbose   = TRUE
    )
    print(res_geno$weights)
    print(res_geno$popdrop)
    print(res_f2$weights)
    print(res_f2$popdrop)
}

merged_HO

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[Vallicanus]

Surely you need to utilise some Cisalpine Celtic or Rhaetic source as well as Central Mediterranean (how would you define this category?) and Langobard/North European.

 

[Jovialis]

 

[Jovialis]

This "C7" cluster based on the PCA looks like a mix of Locals with North of Alps admixture. Which is more suitable than straight up Northern European Langobard admixture.

 

[Vallicanus]

View attachment 18523
View attachment 18524

Where would you draw the border between North and Central Italy...along the Tuscany-Emilia border or further south?

 

[Pax Augusta]

Where would you draw the border between North and Central Italy...along the Tuscany-Emilia border or further south?

Likely further south. Genetic boundaries in Italy are blurred, as a clinal gradient exists throughout the country, sometimes even within the same region. The genetic border between northern and central Italy (see also post #126), in a clinal sense, may lie between somewhere in (southern) Tuscany and the median language group (Umbria, Marche, Lazio). It is unlikely to be along the Tuscany-Emilia border.

This was posted by Jovials.

TSI originates from the province of Florence (exact locality unknown), while modern samples from Murlo, Casentino, and Volterra were labeled "Tuscan" in earlier studies, so Tuscan_1 may correspond to these. Tuscan HGDP, according to CEPH coordinates, comes from the province of Grosseto and is included in the Italian_North group (which also includes samples from the Po Valley, Pre-Alps, and Alps). Notably, no samples from northwest Tuscany or Tosco-Emilian Appennines are present in the studies. In my view, samples along the Tuscany-Emilia border would be even closer to the northern Italian average. It is unlikely that they mark the boundary between northern and central Italy, as even samples from areas further south in Tuscany than the Tuscany-Emilia border fall within the northern Italian macro-cluster (see Raveane 2019).

The Italian_central group, samples chosen by geneticists, includes six individuals labeled as Southern Tuscany in the studies, but these are all from areas bordering Umbria, such as Chiusi, Bettolle, and Ca' De Cio—localities within a few kilometers of Umbria. However, when plotted in a PCA, as I recall, these samples do not align with the Italian_central group but are closer to other Tuscan samples. The remaining samples in the Italian_central group come from the province of Perugia (Umbria), Lake Bolsena in the province of Viterbo (Lazio), two from the province of Ancona, and one from the province of Ascoli Piceno (Marche).

In contrast, the Italian_North group, samples chosen by geneticists, includes, in addition to Tuscan HGDP and Bergamo HGDP, samples from Emilia-Romagna (Modena, Piacenza, Borgonovo Val Tidone (Piacenza), Borgo Val di Taro (Parma), Busseto (Parma), Parma, Ferrara), with no samples from the province of Bologna or Romagna, Veneto (Bassano del Grappa, Vicenza, Treviso), Friuli-Venezia Giulia (Sappada, a linguistic minority), Piedmont (Turin, Alessandria, Cuneo, Domodossola), Lombardy (Cremona, Vernate (Milan), Bergamo), and Trentino-Alto Adige (Nogarè and Taio, Trento). Likely the Alps and Pre-Alps are overrepresented in the Italian_North group, while samples from the Po Valley and Adriatic coast, where the majority of northern Italians reside, are a bit underrepresented.

 

[Jovialis]

Where would you draw the border between North and Central Italy...along the Tuscany-Emilia border or further south?

"North" is Italian_North.HO, which includes Tuscans, but also far north populations. Center is non-Tuscans.

 

[Pax Augusta]

This "C7" cluster based on the PCA looks like a mix of Locals with North of Alps admixture. Which is more suitable than straight up Northern European Langobard admixture.

Is C7 also the most similar to Iron Age profile (Etruscans, Latins, Picenes...)?

 

[Jovialis]

Is C7 also the most similar to Iron Age profile (Etruscans, Latins, Picenes...)?

I would assume that it could be at least a good portion if not majority. C6 can also be modeled as partly Italic (30-50%) with a Greek/Aegean-like component.

I would like to make a model with picenes when possible.

 

[Jovialis]

Here's a model that uses Italy_BA.SG (Italic from Monopoli, in Bari) along with EMBA Cretens (Minoans); which basically act as a proxy for the Greek/Aegean-like influence.

 

[Jovialis]

Here's a model that uses Italy_BA.SG (Italic from Monopoli, in Bari) along with EMBA Cretens (Minoans); which basically act as a proxy for the Greek/Aegean-like influence.
View attachment 18525

The Imperial Era C6 cluster can be model almost identically to Modern Southern Italians using Italy_BA.SG +EMBA_Crete:

 

[Jovialis]

 

[Jovialis]

Interesting model for Italian_North.HO using France_Metz_GalloRoman.SG with Medieval C6 and Italy_Bivio_Roman.SG

 

[Vallicanus]

Is C7 really equivalent to 43.2% Germanic Langobard?

I would have thought Latini_IA would have covered most (or all) of the C7 category.

 

[Jovialis]

Is C7 really equivalent to 43.2% Germanic Langobard?

I would have thought Latini_IA would have covered most (or all) of the C7 category.

Better proxies would likely consume more of it; either a better Italic and/or Celtic population to add.